Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response

ABSTRACT: The goal of this experiment was to determine how dopamine receptor activation in medium spiny neurons alters rapid transcriptional programs. To identify genes altered by dopamine, we used a rat primary striatal neuronal culture system in which striatal neurons were removed from the rat brain at embryonic day 18, cultured for 11 days in vitro using standard neuronal conditions, and treated neurons with either vehicle (neurobasal media) or dopamine (at a concentration of 1µM) for 1hr. This dataset contains PolyA+ RNA-seq results from this experiment, in which we identified 100 upregulated genes and 3 downregulated genes after dopamine stimulation using DESeq2 pipelines.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE137568 | GEO | 2020/06/24

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq datasets for enhancer RNA quantification in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems"

Project description:This dataset contains total RNA sequencing results from rat embryonic cortical, hippocampal, and striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 1hr prior to RNA extraction.

2020-07-28 | GSE150499 | GEO

ATAC-seq datasets for chromatin accessibility quantification in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems"

Project description:This dataset contains Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat embryonic cortical, hippocampal, and striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 1hr.

2020-07-28 | GSE150589 | GEO

Striatal cultured neurons single-nucleus RNA-seq dataset for "A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response"

Project description:This dataset contains single-nucleus RNA sequencing results from rat embryonic striatal neuronal cultures and serves as the basis for characterization of transcriptional response to dopamine (50µM), the Drd1 agonist SKF-38393 (1µM), and potassium chloride (25mM). The goal of this experiment was to define the transcriptional response to each of these stimulations across distinct cell types in cultured neurons. Single-cell sequencing was carried out on FACS-sorted nuclei isolated from these experiments using the 10X Genomics Chromium single cell sequencing platform.

2020-06-24 | GSE137759 | GEO

RNA-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer" [RNA-seq]

Project description:This dataset contains RNA-seq results from rat embryonic striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 4 h.

2023-08-07 | GSE233752 | GEO

RNA-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer"

Project description:This dataset contains Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat embryonic striatal neuronal cultures treated with either vehicle (complete Neurobasal media) or potassium chloride (10mM) for 4 h.

2023-08-07 | GSE233368 | GEO

Effect of bromodomain inhibitors on dopamine D1R induced gene expression in striatal neurons

Project description:The dopamine D1R is Gs coupled GPCR which is expressed in striatal neurons and stimulates gene expression upon activation by dopamine or other agonists. In this work we investigated the role of the BET protein bromodomain containing protein 4 (Brd4) in mediating D1R-dependent gene expression in rat striatal neurons. Here we report the results of 3 RNA sequencing experiments. In Experiment 1 we treated primary striatal neurons with the D1R-selective agonist SKF-81297 alone or in combination with the non-selective BET inhibitor JQ1 for 60 minutes to assess the effect of BET inhibition on acute D1R-dependent gene expression. In Experiment 2, we treated primary striatal neurons with the D1R-selective agonist SKF-81297 alone or in combination with the BET bromodomain 2 selective inhibitor iBD2 for 60 minutes to determine the contribution of BD2 specifically to D1R-dependent gene expression. In Experiment 3 we treated primary striatal neurons with the D1R-selective agonist SKF-81297 alone or in combination with the non-selective BET inhibitor JQ1 for 24 hours to assess the effect of prolonged BET inhibition on basal gene expression and D1R-dependent gene expression.

2021-07-05 | GSE179370 | GEO

Dopaplex RNA-seq dataset for "A dopamine-induced coordinated gene expression program regulates neuronal function and cocaine response"

Project description:This dataset contains whole-genome RNA sequencing results from rat embryonic striatal neuronal cultures and serves as the basis for characterization of multiplexed CRISPR/dCas9 gene activation of 16 genes induced by dopamine receptor activation. The goal of this experiment was to define the transcriptional response to multiplexed CRISPR-based upregulation of 16 dopamine-induced genes (Tent5b, Junb, Prox1, Nr4a2, Nptx1, Gsx1, Gadd45g, Btg2, Fosb, Nr4a1, Egr4, Fos, Sstr2, Gadd45b, Egr3, & Egr2), together termed "Dopaplex", as compared to a LacZ control sgRNA.

2020-06-24 | GSE137658 | GEO

Mesocorticolimbic circuit mechanisms underlying the effects of ketamine on dopamine: a translational imaging study

Project description:Patients with schizophrenia show increased striatal dopamine synthesis capacity in imaging studies. However, the mechanism underlying this is unclear but may be due to N-methyl-D-aspartate receptor (NMDAR) hypofunction and parvalbumin (PV) neuronal dysfunction leading to disinhibition of mesostriatal dopamine neurons. Here, we test this in a translational mouse imaging study using a ketamine model. Mice were treated with sub-chronic ketamine (30mg/kg) or saline followed by in-vivo positron emission tomography of striatal dopamine synthesis capacity, analogous to measures used in patients. Locomotor activity was measured using the open field test. In-vivo cell-type-specific chemogenetic approaches and pharmacological interventions were used to manipulate neuronal excitability. Immunohistochemistry and RNA sequencing were used to investigate molecular mechanisms. Sub-chronic ketamine increased striatal dopamine synthesis capacity (Cohen’s d=2.5) and locomotor activity. These effects were countered by inhibition of midbrain dopamine neurons, and by activation of cortical and ventral subiculum PV interneurons. Sub-chronic ketamine reduced PV expression in these neurons. Pharmacological intervention with SEP-363856, a novel psychotropic agent with agonism at trace amine receptor 1 (TAAR1), significantly reduced the ketamine-induced increase in dopamine synthesis capacity. These results show that sub-chronic ketamine treatment in mice mimics the dopaminergic alterations in patients with psychosis, and suggest an underlying neurocircuit involving PV interneuron hypofunction in frontal cortex and hippocampus as well as activation of midbrain dopamine neurons. A novel TAAR1 agonist reversed the dopaminergic alterations suggesting a therapeutic mechanism for targeting presynaptic dopamine dysfunction in patients.

2021-02-16 | GSE138802 | GEO

DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons

Project description:Neuronal DNA modifications differ from those in other cells, including methylation outside CpG context and abundant 5-hydroxymethylation whose relevance for neuronal identities are unclear. Striatal projection neurons expressing D1 or D2 dopamine receptors allow addressing this question, as they share many characteristics but differ in their gene expression profiles, connections, and functional roles. We compare translating mRNAs and DNA modifications in these two populations. DNA methylation differences occur predominantly in large genomic clusters including differentially expressed genes, potentially important for D1 and D2 neurons. Decreased gene body methylation is associated with higher gene expression. Hydroxymethylation differences are more scattered and affect transcription factor binding sites, which can influence gene expression. We also find a strong genome-wide hydroxymethylation asymmetry between the two DNA strands, particularly pronounced at expressed genes and retrotransposons. These results identify novel properties of neuronal DNA modifications and unveil epigenetic characteristics of striatal projection neurons heterogeneity.

2022-11-11 | GSE186572 | GEO

Gene expression profile of 2-D or 3-D neural cultures derived from an H1 hESC cell line

Project description:Striatal neurons and striatal DA neuron fusions make up the mesolimbic pathway and respond to substances of abuse. We use scRNAseq to define the composition of our culture conditions and study their transcriptional responses to dopamine, cocaine, and morphine.

2023-04-14 | GSE225497 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data